cpdb: Get residue contacts Package

Description

This R package allows the user to get the intramolecular contacts of a specific residue from a solved PDB protein structure. Its use is intended to researchers in genetic mutations.

How to use

Install the package

library(devtools)
devtools::install_github("karlapenag/cpdb", build_vignettes = TRUE)

library(cpdb)

get_contacts() function

This function has four arguments,pdb, chain, res and a.

pdb and chain have to be strings. The default for chain is "A". res is the position number of the residue in the protein sequence. a is the distance in angstroms. Default = 8.

returns a text with the residue contacts.

plot_closest() function

This function has the same four arguments,pdb, chain, res and a.

pdb and chain have to be strings. The default for chain is "A". res is the position number of the residue in the protein sequence. a is the distance in angstroms. Default = 8.

returns a ´plot´ of the closest residues to the target residue.

get_contacts("4q21", "A", 15, 6)
#>   Note: Accessing on-line PDB file
#> [1] "The residue contacts positions are:"
#> [1] 13 14 16 17 18 19

plot_closest("4q21", "A", 15, 8)
#>   Note: Accessing on-line PDB file
#> Warning in get.pdb(file, path = tempdir(), verbose = FALSE): /var/folders/mk/
#> flrx70c914z_hflv_j2q0d8h0000gn/T//RtmpXIBXxg/4q21.pdb exists. Skipping download